Neda Bagheri

Title(s)Lab Ast 2, Pathology
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions. PLoS Comput Biol. 2024 Mar 08; 20(3):e1011917. Yu JS, Bagheri N. PMID: 38457450.
      View in: PubMed   Mentions:    Fields:    
    2. Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence. Bioinformatics. 2024 Mar 05. Cain JY, Evarts JI, Yu JS, Bagheri N. PMID: 38444088.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    3. PAM-Engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications. Angew Chem Int Ed Engl. 2024 Jan 29; e202319677. Bagheri N, Chamorro A, Idili A, Porchetta A. PMID: 38284432.
      View in: PubMed   Mentions:    Fields:    
    4. Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing. Adv Biochem Eng Biotechnol. 2024 Jan 26. Chamorro A, Rossetti M, Bagheri N, Porchetta A. PMID: 38273204.
      View in: PubMed   Mentions:    Fields:    
    5. Energy metabolism modulates the regulatory impact of activators on gene expression. Development. 2024 Jan 01; 151(1). Qiao S, Bernasek S, Gallagher KD, O'Connell J, Yamada S, Bagheri N, Amaral LAN, Carthew RW. PMID: 38063847; PMCID: PMC10820824.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    6. Energy metabolism modulates the regulatory impact of activators on gene expression. bioRxiv. 2023 Oct 26. Qiao S, Bernasek S, Gallagher KD, Yamada S, Bagheri N, Amaral LAN, Carthew RW. PMID: 37961620; PMCID: PMC10634812.
      View in: PubMed   Mentions:
    7. Minimalist Design of Wireframe DNA Nanotubes: Tunable Geometry, Size, Chirality, and Dynamics. Angew Chem Int Ed Engl. 2023 10 26; 62(44):e202309869. Luo X, Saliba D, Yang T, Gentile S, Mori K, Islas P, Das T, Bagheri N, Porchetta A, Guarne A, Cosa G, Sleiman HF. PMID: 37610293.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    8. Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila. Development. 2023 04 15; 150(8). Bernasek SM, Hur SSJ, Peláez-Restrepo N, Boisclair Lachance JF, Bakker R, Navarro HT, Sanchez-Luege N, Amaral LAN, Bagheri N, Rebay I, Carthew RW. PMID: 36942737; PMCID: PMC10163347.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    9. A smart paper-based electrochemical sensor for reliable detection of iron ions in serum. Anal Bioanal Chem. 2023 Mar; 415(6):1149-1157. Mazzaracchio V, Bagheri N, Chiara F, Fiore L, Moscone D, Roggero S, Arduini F. PMID: 36700985.
      View in: PubMed   Mentions: 1     Fields:    
    10. The in silico lab: Improving academic code using lessons from biology. Cell Syst. 2023 01 18; 14(1):1-6. Cain JY, Yu JS, Bagheri N. PMID: 36657389.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    11. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res. 2022 08 12; 50(14):8377-8391. Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. PMID: 35822842; PMCID: PMC9371913.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    12. Mapping CAR T-Cell Design Space Using Agent-Based Models. Front Mol Biosci. 2022; 9:849363. Prybutok AN, Yu JS, Leonard JN, Bagheri N. PMID: 35903149; PMCID: PMC9315201.
      View in: PubMed   Mentions: 6  
    13. Correction to "GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems". ACS Synth Biol. 2022 Apr 15; 11(4):1699-1704. Dray KE, Muldoon JJ, Mangan NM, Bagheri N, Leonard JN. PMID: 35271255; PMCID: PMC9119373.
      View in: PubMed   Mentions:    Fields:    
    14. Effect of Preoperative Administration of Oral Melatonin on Pneumatic Tourniquet-Induced Ischemia-Reperfusion Injury in Orthopedic Surgery of Lower Extremities: A Randomized Clinical Trial. Iran J Med Sci. 2022 03; 47(2):123-130. Jouybar R, Khademi S, Razmjooie S, Bagheri N. PMID: 35291433; PMCID: PMC8919302.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    15. Fighting fire with fire: deploying complexity in computational modeling to effectively characterize complex biological systems. Curr Opin Biotechnol. 2022 06; 75:102704. Prybutok AN, Cain JY, Leonard JN, Bagheri N. PMID: 35231773.
      View in: PubMed   Mentions: 1     Fields:    
    16. The new era of quantitative cell imaging-challenges and opportunities. Mol Cell. 2022 01 20; 82(2):241-247. Bagheri N, Carpenter AE, Lundberg E, Plant AL, Horwitz R. PMID: 35063094; PMCID: PMC10339817.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    17. GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems. ACS Synth Biol. 2022 02 18; 11(2):1009-1029. Dray KE, Muldoon JJ, Mangan NM, Bagheri N, Leonard JN. PMID: 35023730; PMCID: PMC9097825.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    18. Morphological features of single cells enable accurate automated classification of cancer from non-cancer cell lines. Sci Rep. 2021 12 21; 11(1):24375. Mousavikhamene Z, Sykora DJ, Mrksich M, Bagheri N. PMID: 34934149; PMCID: PMC8692621.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    19. Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model. Cell Syst. 2021 08 18; 12(8):795-809.e9. Yu JS, Bagheri N. PMID: 34139155.
      View in: PubMed   Mentions: 5     Fields:    
    20. Multi-array wax paper-based platform for the pre-concentration and determination of silver ions in drinking water. Talanta. 2021 Sep 01; 232:122474. Bagheri N, Cinti S, Nobile E, Moscone D, Arduini F. PMID: 34074442.
      View in: PubMed   Mentions: 3     Fields:    
    21. Electroanalytical Sensor Based on Gold-Nanoparticle-Decorated Paper for Sensitive Detection of Copper Ions in Sweat and Serum. Anal Chem. 2021 03 30; 93(12):5225-5233. Bagheri N, Mazzaracchio V, Cinti S, Colozza N, Di Natale C, Netti PA, Saraji M, Roggero S, Moscone D, Arduini F. PMID: 33739824.
      View in: PubMed   Mentions: 12     Fields:    
    22. Agent-Based Models Predict Emergent Behavior of Heterogeneous Cell Populations in Dynamic Microenvironments. Front Bioeng Biotechnol. 2020; 8:249. Yu JS, Bagheri N. PMID: 32596213; PMCID: PMC7301008.
      View in: PubMed   Mentions: 14  
    23. Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila. PLoS Comput Biol. 2020 03; 16(3):e1007406. Bernasek SM, Peláez N, Carthew RW, Bagheri N, Amaral LAN. PMID: 32126077; PMCID: PMC7100978.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    24. Macrophages employ quorum licensing to regulate collective activation. Nat Commun. 2020 02 13; 11(1):878. Muldoon JJ, Chuang Y, Bagheri N, Leonard JN. PMID: 32054845; PMCID: PMC7018708.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    25. The COMET toolkit for composing customizable genetic programs in mammalian cells. Nat Commun. 2020 02 07; 11(1):779. Donahue PS, Draut JW, Muldoon JJ, Edelstein HI, Bagheri N, Leonard JN. PMID: 32034124; PMCID: PMC7005830.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    26. DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data. Bioinformatics. 2019 12 15; 35(24):5103-5112. Xue AY, Yu AM, Lucks JB, Bagheri N. PMID: 31389563; PMCID: PMC6954663.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    27. Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights. Bioinformatics. 2019 11 01; 35(22):4671-4678. Finkle JD, Bagheri N. PMID: 30994899; PMCID: PMC6853664.
      View in: PubMed   Mentions:    Fields:    
    28. Combining gold nanoparticle-based headspace single-drop microextraction and a paper-based colorimetric assay for selenium determination. Anal Bioanal Chem. 2019 Nov; 411(28):7441-7449. Bagheri N, Saraji M. PMID: 31654101.
      View in: PubMed   Mentions: 4     Fields:    
    29. Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants. Bioinformatics. 2019 09 15; 35(18):3421-3432. Muldoon JJ, Yu JS, Fassia MK, Bagheri N. PMID: 30932143; PMCID: PMC6748731.
      View in: PubMed   Mentions: 3     Fields:    
    30. Repressive Gene Regulation Synchronizes Development with Cellular Metabolism. Cell. 2019 08 08; 178(4):980-992.e17. Cassidy JJ, Bernasek SM, Bakker R, Giri R, Peláez N, Eder B, Bobrowska A, Bagheri N, Nunes Amaral LA, Carthew RW. PMID: 31353220; PMCID: PMC6865806.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    31. Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia. Am J Respir Crit Care Med. 2019 05 15; 199(10):1225-1237. Walter JM, Ren Z, Yacoub T, Reyfman PA, Shah RD, Abdala-Valencia H, Nam K, Morgan VK, Anekalla KR, Joshi N, McQuattie-Pimentel AC, Chen CI, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Aillon RP, Watanabe S, Williams KJN, Lu Z, Paonessa J, Hountras P, Breganio M, Borkowski N, Donnelly HK, Allen JP, Amaral LA, Bharat A, Misharin AV, Bagheri N, Hauser AR, Budinger GRS, Wunderink RG. PMID: 30398927; PMCID: PMC6519857.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    32. A 96-well wax printed Prussian Blue paper for the visual determination of cholinesterase activity in human serum. Biosens Bioelectron. 2019 Jun 01; 134:97-102. Bagheri N, Cinti S, Caratelli V, Massoud R, Saraji M, Moscone D, Arduini F. PMID: 30959394.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    33. Exploration of the nanomedicine-design space with high-throughput screening and machine learning. Nat Biomed Eng. 2019 04; 3(4):318-327. Yamankurt G, Berns EJ, Xue A, Lee A, Bagheri N, Mrksich M, Mirkin CA. PMID: 30952978; PMCID: PMC6452897.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    34. Windowed Granger causal inference strategy improves discovery of gene regulatory networks. Proc Natl Acad Sci U S A. 2018 02 27; 115(9):2252-2257. Finkle JD, Wu JJ, Bagheri N. PMID: 29440433; PMCID: PMC5834671.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    35. Multiplexing Engineered Receptors for Multiparametric Evaluation of Environmental Ligands. ACS Synth Biol. 2017 11 17; 6(11):2042-2055. Hartfield RM, Schwarz KA, Muldoon JJ, Bagheri N, Leonard JN. PMID: 28771312; PMCID: PMC5693605.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCellsPHPublic Health
    36. Machine Learning on Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry. Anal Chem. 2017 09 05; 89(17):9039-9047. Xue AY, Szymczak LC, Mrksich M, Bagheri N. PMID: 28719743; PMCID: PMC5588089.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    37. Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span. J Exp Med. 2017 Aug 07; 214(8):2387-2404. Misharin AV, Morales-Nebreda L, Reyfman PA, Cuda CM, Walter JM, McQuattie-Pimentel AC, Chen CI, Anekalla KR, Joshi N, Williams KJN, Abdala-Valencia H, Yacoub TJ, Chi M, Chiu S, Gonzalez-Gonzalez FJ, Gates K, Lam AP, Nicholson TT, Homan PJ, Soberanes S, Dominguez S, Morgan VK, Saber R, Shaffer A, Hinchcliff M, Marshall SA, Bharat A, Berdnikovs S, Bhorade SM, Bartom ET, Morimoto RI, Balch WE, Sznajder JI, Chandel NS, Mutlu GM, Jain M, Gottardi CJ, Singer BD, Ridge KM, Bagheri N, Shilatifard A, Budinger GRS, Perlman H. PMID: 28694385; PMCID: PMC5551573.
      View in: PubMed   Mentions: 472     Fields:    Translation:HumansAnimalsCells
    38. Modulating and evaluating receptor promiscuity through directed evolution and modeling. Protein Eng Des Sel. 2017 06 01; 30(6):455-465. Stainbrook SC, Yu JS, Reddick MP, Bagheri N, Tyo KEJ. PMID: 28453776; PMCID: PMC6283399.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    39. Multi-class and multi-scale models of complex biological phenomena. Curr Opin Biotechnol. 2016 06; 39:167-173. Yu JS, Bagheri N. PMID: 27115496.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimals
    40. Osteopetrosis in siblings. Intern Emerg Med. 2016 Jun; 11(4):615-6. Mosayebi Z, Mirfazaelian H, Khademi B, Bagheri N, Daneshbod Y. PMID: 26531308.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    41. The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. Integr Biol (Camb). 2015 Jul; 7(7):776-91. Ciaccio MF, Chen VC, Jones RB, Bagheri N. PMID: 26057728; PMCID: PMC4511116.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    42. Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation. Biotechnol Bioeng. 2014 Oct; 111(10):2082-94. Duncan MT, Shin S, Wu JJ, Mays Z, Weng S, Bagheri N, Miller WM, Shea LD. PMID: 24853077; PMCID: PMC4232189.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    43. A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture. Integr Comp Biol. 2014 Jul; 54(2):296-306. Ciaccio MF, Finkle JD, Xue AY, Bagheri N. PMID: 24813462; PMCID: PMC4148605.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    44. Polyfunctional responses by human T cells result from sequential release of cytokines. Proc Natl Acad Sci U S A. 2012 Jan 31; 109(5):1607-12. Han Q, Bagheri N, Bradshaw EM, Hafler DA, Lauffenburger DA, Love JC. PMID: 22160692; PMCID: PMC3277116.
      View in: PubMed   Mentions: 146     Fields:    Translation:HumansCells
    45. Problem of foreign body in GI tract. ScientificWorldJournal. 2011; 11:2147-9. Daneshbod Y, Talei A, Negahban S, Soleimanpour H, Aledavoud A, Bagheri N, Khanlari M, Daneshbod K. PMID: 22125463; PMCID: PMC3217610.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    46. A dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition. PLoS Comput Biol. 2011 Feb; 7(2):e1001085. Bagheri N, Shiina M, Lauffenburger DA, Korn WM. PMID: 21379332; PMCID: PMC3040662.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    47. Prenatal presentation of a metastasizing rhabdoid tumor with homozygous deletion of the SMARCB1 gene. J Clin Oncol. 2010 Nov 20; 28(33):e688-91. Negahban S, Nagel I, Soleimanpour H, Aledavood A, Bagheri N, Paydar M, Daneshbod K, Hasselblatt M, Gesk S, Siebert R, Daneshbod Y. PMID: 20805448.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    48. Modeling the Drosophila melanogaster circadian oscillator via phase optimization. J Biol Rhythms. 2008 Dec; 23(6):525-37. Bagheri N, Lawson MJ, Stelling J, Doyle FJ. PMID: 19060261; PMCID: PMC2675948.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    49. Synchrony and entrainment properties of robust circadian oscillators. J R Soc Interface. 2008 Aug 06; 5 Suppl 1:S17-28. Bagheri N, Taylor SR, Meeker K, Petzold LR, Doyle FJ. PMID: 18426774; PMCID: PMC2706452.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    50. Circadian phase resetting via single and multiple control targets. PLoS Comput Biol. 2008 Jul 04; 4(7):e1000104. Bagheri N, Stelling J, Doyle FJ. PMID: 18795146; PMCID: PMC2536509.
      View in: PubMed   Mentions: 16     Fields:    Translation:Animals
    51. Quantitative performance metrics for robustness in circadian rhythms. Bioinformatics. 2007 Feb 01; 23(3):358-64. Bagheri N, Stelling J, Doyle FJ. PMID: 17158515.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
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